Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001258.1 Hibiscus syriacus cultivar Beakdansim tig00002476_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 144162
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2279 original size:14 final size:15
Alignment explanation
Indices: 2257--2294 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2247 TATTCTTATT
*
2257 AGATGACAA-TGTTG
1 AGATTACAATTGTTG
*
2271 AGATTACAATTTTTG
1 AGATTACAATTGTTG
2286 AGATTACAA
1 AGATTACAA
2295 ATTCGTATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34
Consensus pattern (15 bp):
AGATTACAATTGTTG
Found at i:2725 original size:20 final size:21
Alignment explanation
Indices: 2686--2734 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
2676 CACCTAACTA
* *
2686 TTGATTTTTTGTATTTGTATT
1 TTGATTTTTTATATTAGTATT
2707 TTGATTTTTTATA-TAGTATT
1 TTGATTTTTTATATTAGTATT
2727 TTGATTTT
1 TTGATTTT
2735 AGTTTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.69
Consensus pattern (21 bp):
TTGATTTTTTATATTAGTATT
Found at i:10530 original size:32 final size:32
Alignment explanation
Indices: 10489--10551 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
10479 ATCATTGAAT
10489 TATCAATATTTTCATATGCTATTGTATGATTC
1 TATCAATATTTTCATATGCTATTGTATGATTC
*
10521 TATCAATATTTTCATATGTTATTGTATGATT
1 TATCAATATTTTCATATGCTATTGTATGATT
10552 TTTCATGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (32 bp):
TATCAATATTTTCATATGCTATTGTATGATTC
Found at i:13335 original size:13 final size:13
Alignment explanation
Indices: 13319--13343 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13309 TCCACCTAGA
13319 CAATCATCACACT
1 CAATCATCACACT
13332 CAATCATCACAC
1 CAATCATCACAC
13344 CCCTCCCTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (13 bp):
CAATCATCACACT
Found at i:18133 original size:31 final size:31
Alignment explanation
Indices: 18086--18169 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
18076 CAAAATAGTG
* *
18086 ATTAAA-TTATCTAACTGTTACAAAACGGTC
1 ATTAAATTTATCGAACTGTTACAAAACGATC
* * * *
18116 ATTTATTTTATCGAACTGTTACGAAATGATC
1 ATTAAATTTATCGAACTGTTACAAAACGATC
* *
18147 ATTAAATTTATTGAACTTTTACA
1 ATTAAATTTATCGAACTGTTACA
18170 CTTATGATAA
Statistics
Matches: 42, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 4 0.10
31 38 0.90
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (31 bp):
ATTAAATTTATCGAACTGTTACAAAACGATC
Found at i:19568 original size:7 final size:7
Alignment explanation
Indices: 19552--19587 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
19542 GGTAAAGTAG
19552 AAAA-GA
1 AAAAGGA
19558 AAAAGGA
1 AAAAGGA
19565 AAAAGGA
1 AAAAGGA
19572 AAAAGGA
1 AAAAGGA
*
19579 AAATGGA
1 AAAAGGA
19586 AA
1 AA
19588 GTGGAAAGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 4 0.14
7 24 0.86
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (7 bp):
AAAAGGA
Found at i:19593 original size:14 final size:14
Alignment explanation
Indices: 19556--19605 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
19546 AAGTAGAAAA
* *
19556 GAAAAAGGAAAAAG
1 GAAAGAGGAAAATG
*
19570 GAAAAAGGAAAATG
1 GAAAGAGGAAAATG
* *
19584 GAAAGTGGAAAGTG
1 GAAAGAGGAAAATG
19598 GAAAGAGG
1 GAAAGAGG
19606 TATCAGGAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.58, C:0.00, G:0.36, T:0.06
Consensus pattern (14 bp):
GAAAGAGGAAAATG
Found at i:25105 original size:20 final size:21
Alignment explanation
Indices: 25080--25128 Score: 91
Period size: 20 Copynumber: 2.4 Consensus size: 21
25070 CTGAACTGAA
25080 AAACAGAAGCATAACAGCTT-
1 AAACAGAAGCATAACAGCTTG
25100 AAACAGAAGCATAACAGCTTG
1 AAACAGAAGCATAACAGCTTG
25121 AAACAGAA
1 AAACAGAA
25129 AACTCAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.53, C:0.18, G:0.16, T:0.12
Consensus pattern (21 bp):
AAACAGAAGCATAACAGCTTG
Found at i:25790 original size:184 final size:184
Alignment explanation
Indices: 25482--25869 Score: 636
Period size: 184 Copynumber: 2.1 Consensus size: 184
25472 TTTTATAATT
* * * * *
25482 TATATAA-AAATTAAATGTTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
25546 TATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* *
25611 GAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGAGCTTAGCCTATATGTTA
131 GAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGAGCTGAGCCCATATGTTA
25665 TATATAATATATTTAATATTTTTTAATTAAAAAAATAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAA
* * *
25730 TTATAAAATAAAAATTTTATAT-AATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
65 TTATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
* *
25794 TGTATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
130 TGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGAGCTGAGCCCATATGTTA
*
25849 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
25870 AAAATTTAAT
Statistics
Matches: 190, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
183 7 0.04
184 134 0.71
185 49 0.26
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
GAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGAGCTGAGCCCATATGTTA
Found at i:28070 original size:54 final size:54
Alignment explanation
Indices: 27958--28070 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
27948 AGTACTCTTG
* * *
27958 TATTATTTGATAGAGTAACAACTTGCTGACTGTGACCAGTATCGGGGGCAGAAT
1 TATTATTTGATAGAGCAACAACTTGCTGACTATGACCAGTATCGGGGGCAGAAC
* ** * *
28012 TATTATTTGATGGAGCAACTGCTTGCTGACTATGACCAGTATTGGGTGCA-AAGC
1 TATTATTTGATAGAGCAACAACTTGCTGACTATGACCAGTATCGGGGGCAGAA-C
28066 TATTA
1 TATTA
28071 GTAATACTGG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
53 2 0.04
54 48 0.96
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (54 bp):
TATTATTTGATAGAGCAACAACTTGCTGACTATGACCAGTATCGGGGGCAGAAC
Found at i:30954 original size:20 final size:21
Alignment explanation
Indices: 30929--30977 Score: 91
Period size: 20 Copynumber: 2.4 Consensus size: 21
30919 CTGAACTGAA
30929 AAACAGAAGCATAACAGCTT-
1 AAACAGAAGCATAACAGCTTG
30949 AAACAGAAGCATAACAGCTTG
1 AAACAGAAGCATAACAGCTTG
30970 AAACAGAA
1 AAACAGAA
30978 AACTCAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.53, C:0.18, G:0.16, T:0.12
Consensus pattern (21 bp):
AAACAGAAGCATAACAGCTTG
Found at i:34933 original size:16 final size:16
Alignment explanation
Indices: 34912--34944 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
34902 TAATAAATAG
34912 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
34928 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
34944 A
1 A
34945 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:35025 original size:10 final size:10
Alignment explanation
Indices: 35010--35084 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
35000 CATTTAATAA
35010 ATAAACGAAC
1 ATAAACGAAC
35020 ATAAACGAAC
1 ATAAACGAAC
35030 ----ACGAAC
1 ATAAACGAAC
35036 ATAAACGAAC
1 ATAAACGAAC
** *
35046 ACGAAC-ATAA
1 ATAAACGA-AC
35056 ATGAACACGAAC
1 AT-AA-ACGAAC
35068 ATAAACGAAC
1 ATAAACGAAC
35078 ATAAACG
1 ATAAACG
35085 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:35035 original size:16 final size:16
Alignment explanation
Indices: 35014--35078 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
35004 TAATAAATAA
35014 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
35030 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
35046 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
35062 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
35078 A
1 A
35079 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:35843 original size:10 final size:10
Alignment explanation
Indices: 35828--35875 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
35818 ATAAATGAAT
35828 GAACATAAAC
1 GAACATAAAC
35838 GAACATAATCGAAC
1 GAACAT-A---AAC
35852 GAACATAAAC
1 GAACATAAAC
*
35862 GAACATAACC
1 GAACATAAAC
35872 GAAC
1 GAAC
35876 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:35852 original size:14 final size:14
Alignment explanation
Indices: 35835--35865 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35825 AATGAACATA
*
35835 AACGAACATAATCG
1 AACGAACATAAACG
35849 AACGAACATAAACG
1 AACGAACATAAACG
35863 AAC
1 AAC
35866 ATAACCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:35855 original size:24 final size:24
Alignment explanation
Indices: 35815--35876 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
35805 GATTGGGTTA
*
35815 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
35839 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
*
35863 AACATAACCGAACG
1 AACATAATCGAACG
35877 TTCACGAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 3 0.09
24 32 0.91
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:39715 original size:29 final size:29
Alignment explanation
Indices: 39678--39759 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
39668 AAAAACAATT
*
39678 TTATAATAATAATTATTAAAA-TTAAAAAA
1 TTATTATAA-AATTATTAAAATTTAAAAAA
* **
39707 TTATTATAAAATTTATCAAAATTTATCAAA
1 TTATTATAAAA-TTATTAAAATTTAAAAAA
* *
39737 TCATTATAAATTTATT-AAATTTA
1 TTATTATAAAATTATTAAAATTTA
39760 CTTAATCAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
28 9 0.20
29 20 0.45
30 15 0.34
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (29 bp):
TTATTATAAAATTATTAAAATTTAAAAAA
Found at i:53148 original size:31 final size:31
Alignment explanation
Indices: 53112--53171 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
53102 ATTAAACTAA
*
53112 TACAAAATGATCATTAAACTTATCAAATTAT
1 TACAAAAGGATCATTAAACTTATCAAATTAT
* *
53143 TACAAAAGGATCCTTAAACTTATTAAATT
1 TACAAAAGGATCATTAAACTTATCAAATT
53172 TATCACCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (31 bp):
TACAAAAGGATCATTAAACTTATCAAATTAT
Found at i:55944 original size:3 final size:3
Alignment explanation
Indices: 55930--55959 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
55920 TTATAATGAT
55930 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
55960 TATTATTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:60902 original size:4 final size:4
Alignment explanation
Indices: 60893--60934 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
60883 ACATCGATCC
*
60893 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT-T -TGT ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
60935 CAGCTTGCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 2 0.06
4 31 0.91
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:61017 original size:88 final size:88
Alignment explanation
Indices: 60915--61117 Score: 297
Period size: 88 Copynumber: 2.3 Consensus size: 88
60905 ATGTATGTAT
*
60915 GTATGTATTTGTATGCATGTCAGCTTGCTAACAACCATTTTCACCGGTACATTTTGTCAGAAAAA
1 GTATGTA-TTGTATGCATGTCAGCTTGCTAACAACCATTTTCACCGGTACATTTTATCAGAAAAA
*
60980 CTCAGAACACATGGAT-CGGGTAC
65 CTCAGAACACATGGATCCAGGTAC
**
61003 GTATGTATCTGTATGCATGTCAGCTTGCTAACAACCATTTTCACTTGTACATTTTATCAGAAAAA
1 GTATGTAT-TGTATGCATGTCAGCTTGCTAACAACCATTTTCACCGGTACATTTTATCAGAAAAA
* * *
61068 CTCGGAACACATGGATCCATGTAT
65 CTCAGAACACATGGATCCAGGTAC
61092 GTATGTA-TG--TGCATGTCAGCTTGCTA
1 GTATGTATTGTATGCATGTCAGCTTGCTA
61118 GGGACGATTG
Statistics
Matches: 106, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
85 17 0.16
87 3 0.03
88 75 0.71
89 11 0.10
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (88 bp):
GTATGTATTGTATGCATGTCAGCTTGCTAACAACCATTTTCACCGGTACATTTTATCAGAAAAAC
TCAGAACACATGGATCCAGGTAC
Found at i:70850 original size:6 final size:6
Alignment explanation
Indices: 70810--70847 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
70800 TTCACGGTCC
* *
70810 GAAGTG GAAGTG GAAGTG GAAGTG GGAGTG GAGGTG GA
1 GAAGTG GAAGTG GAAGTG GAAGTG GAAGTG GAAGTG GA
70848 GGTAGGGCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.55, T:0.16
Consensus pattern (6 bp):
GAAGTG
Found at i:72444 original size:28 final size:28
Alignment explanation
Indices: 72387--72445 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
72377 CATTGCAGTT
* *
72387 TATTTCAAGCACTGACTCAATAACATAA
1 TATTTCAAGCACTGACTCAACAACACAA
* * *
72415 TATTTCAAGCACTGGCTCGACGACACAA
1 TATTTCAAGCACTGACTCAACAACACAA
72443 TAT
1 TAT
72446 AAACGGAGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (28 bp):
TATTTCAAGCACTGACTCAACAACACAA
Found at i:72941 original size:35 final size:35
Alignment explanation
Indices: 72895--72969 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
72885 ATCGAAGTTT
*
72895 TTTTTTTTGATTAATCAGTCGATTAACAATTAAAG
1 TTTTGTTTGATTAATCAGTCGATTAACAATTAAAG
*
72930 TTTTGTTTGATTAATCAGTCGATTAACAGTTAAAG
1 TTTTGTTTGATTAATCAGTCGATTAACAATTAAAG
72965 TTTTG
1 TTTTG
72970 CTCAAATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.47
Consensus pattern (35 bp):
TTTTGTTTGATTAATCAGTCGATTAACAATTAAAG
Found at i:74873 original size:21 final size:21
Alignment explanation
Indices: 74847--74891 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
74837 GATTTCTGGG
* *
74847 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
74868 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
74889 CAA
1 CAA
74892 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:75454 original size:2 final size:2
Alignment explanation
Indices: 75447--75495 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
75437 CATGAGTTAG
75447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75489 AT AT AT A
1 AT AT AT A
75496 GGAATTGTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:76049 original size:31 final size:30
Alignment explanation
Indices: 75991--76068 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
75981 AGAGTCGAGG
* *
75991 GTTTACCTATGTCTTTCGAGACATATGGATA
1 GTTTACCTAGGTC-TTCGAGACATATGGACA
* *
76022 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGG-TCTTCGAGACATATGGACA
* *
76053 ATTTACCGAGGATCTT
1 GTTTACCTAGG-TCTT
76069 TATGACCTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 37 0.95
32 2 0.05
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (30 bp):
GTTTACCTAGGTCTTCGAGACATATGGACA
Found at i:76091 original size:30 final size:30
Alignment explanation
Indices: 76041--76140 Score: 139
Period size: 30 Copynumber: 3.3 Consensus size: 30
76031 GGTTCTTCGG
* *
76041 GACCTATGGACAATTTACCGAGGATCTTTAT
1 GACCTCTGGAC-AGTTACCGAGGATCTTTAT
76072 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
76102 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
76131 GACCTCTGGA
1 GACCTCTGGA
76141 TAGGTCCTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 18 0.28
30 36 0.56
31 10 0.16
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:76137 original size:29 final size:30
Alignment explanation
Indices: 76055--76143 Score: 144
Period size: 30 Copynumber: 3.0 Consensus size: 30
76045 TATGGACAAT
*
76055 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
76085 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
* *
76115 TTACCG-GGGTCTTTGTGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
76144 GTCCTTCGGG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 21 0.38
30 35 0.62
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACCTCTGGATAG
Found at i:77217 original size:21 final size:21
Alignment explanation
Indices: 77175--77217 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
77165 TTTTCGGGCT
* * *
77175 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
77196 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
77217 A
1 A
77218 CGAATATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:77277 original size:66 final size:66
Alignment explanation
Indices: 77197--77344 Score: 253
Period size: 66 Copynumber: 2.2 Consensus size: 66
77187 ACCCATTCAA
*
77197 GGGGAACCGATACCCCCTCAACGAATATGATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA-
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATA-CCCCAG
77261 GG
65 GG
*
77263 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGTGGGGAATCGATACCCCAGG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGG
77328 G
66 G
*
77329 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
77345 ATGAAAAAAA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
65 5 0.06
66 73 0.94
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGG
G
Found at i:78019 original size:23 final size:23
Alignment explanation
Indices: 77953--78011 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
77943 ATCATTATAT
*
77953 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
77975 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
77998 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
78012 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:84096 original size:21 final size:21
Alignment explanation
Indices: 84054--84096 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
84044 TTTTCGGGCT
* * *
84054 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
84075 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
84096 A
1 A
84097 CGAATATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:84156 original size:66 final size:66
Alignment explanation
Indices: 84076--84223 Score: 253
Period size: 66 Copynumber: 2.2 Consensus size: 66
84066 ACCCATTCAA
*
84076 GGGGAACCGATACCCCCTCAACGAATATGATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA-
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATA-CCCCAG
84140 GG
65 GG
*
84142 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGTGGGGAATCGATACCCCAGG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGG
84207 G
66 G
*
84208 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
84224 ATGAAAAAAA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
65 5 0.06
66 73 0.94
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGG
G
Found at i:84898 original size:23 final size:23
Alignment explanation
Indices: 84832--84890 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
84822 ATCATTATAT
*
84832 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
84854 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
84877 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
84891 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:94403 original size:31 final size:31
Alignment explanation
Indices: 94360--94423 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
94350 ATGTGATCAC
*
94360 CTAAAAATTTGAACT-ACTATAAATGCCTCAT
1 CTAAAAAGTTGAACTAAC-ATAAATGCCTCAT
*
94391 CTAAAAAGTTGAACTAACATAAATGCTTCAT
1 CTAAAAAGTTGAACTAACATAAATGCCTCAT
94422 CT
1 CT
94424 TTAACTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (31 bp):
CTAAAAAGTTGAACTAACATAAATGCCTCAT
Found at i:94679 original size:14 final size:15
Alignment explanation
Indices: 94660--94701 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
94650 TATAGTTTAT
94660 ACTATGTAATATA-A
1 ACTATGTAATATACA
*
94674 ACTATGCAATATACA
1 ACTATGTAATATACA
*
94689 ACTATTTAATATA
1 ACTATGTAATATA
94702 TAATACAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.36
Consensus pattern (15 bp):
ACTATGTAATATACA
Found at i:111467 original size:13 final size:14
Alignment explanation
Indices: 111438--111464 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
111428 TTTTAGACTA
111438 ATATTAGCCGCCCC
1 ATATTAGCCGCCCC
111452 ATATTAGCCGCCC
1 ATATTAGCCGCCC
111465 ATAAACTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (14 bp):
ATATTAGCCGCCCC
Found at i:119639 original size:30 final size:29
Alignment explanation
Indices: 119581--119672 Score: 94
Period size: 31 Copynumber: 3.0 Consensus size: 29
119571 TTTTATGATC
* *
119581 ATAAAATTTAATAAATTTATTGACCATTTT
1 ATAAAATTTGATAAATTTA-TAACCATTTT
119611 ATAACAATTTGATAAATTTATAACCATTTTT
1 ATAA-AATTTGATAAATTTATAACCA-TTTT
* * *
119642 GTAAAAGTTCGATAAATTTAATAACTATTTT
1 ATAAAA-TTTGATAAATTT-ATAACCATTTT
119673 GTAATACCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
30 11 0.21
31 36 0.68
32 6 0.11
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (29 bp):
ATAAAATTTGATAAATTTATAACCATTTT
Found at i:140105 original size:2 final size:2
Alignment explanation
Indices: 140100--140172 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
140090 TATTTTAGTC
*
140100 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
140142 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
140173 GTTTATTAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.